Bacteriophages (hereafter referred as phages) can translate their mRNAs efficiently by maximizing the use of codons decoded by the most abundant tRNAs of their bacterial hosts. Translation efficiency directly influences phage fitness and evolution. Reengineered phages find application in controlling their host population in both health and industry. The objective of this thesis work is to examine the factors shaping codon choices of single stranded DNA (ssDNA) and double stranded DNA (dsDNA) Escherichia coli phages. In chapter two, we employed two indices, rRSCU (correlation in relative synonymous codon usage between phages and their hosts) and CAI (codon adaptation index) to measure codon adaptation in phages. None of the analyzed ssDNA phages encode tRNAs while some dsDNA phages encode their own tRNAs. Both rRSCU and CAI are negatively correlated with number of tRNA genes encoded by these dsDNA phages. We observed significantly greater rRSCU for dsDNA phages (without tRNAs) than ssDNA phages. In addition, we propose that ssDNA phages have evolved a novel codon adaptation strategy to overcome the disruptive effect of their high C→T mutation rates in codon adaptation with host. In chapter three, we formulated an index phi to measure selection by host translation machinery and to present explicit linear and nonlinear models to characterize the effect of C→T mutation and host-tRNA-mediated selection on phage codon usage. The effect of selection (phi) on codon usage is detectable in most dsDNA and ssDNA phage species. C→T mutations also interfere with nonsynonymous substitutions at second codon positions, especially in ssDNA phages. Strand asymmetry along with the accompanying local variation in mutation bias can significantly affect codon adaptation in both dsDNA and ssDNA phages.

Sexual conflict is broadly defined as a conflict between the evolutionary interests of the two sexes. Depending on the genetic architecture of the traits involved, it can occur at the level of male-female interactions or take the form of selection acting to change the mean of a shared trait against the sign of its genetic correlation. The aim of my thesis was to use genome-wide expression profiles in the model organism Drosophila melanogaster to provide novel insights in the study of sexual conflict. First, we studied the female post-mating response to partition transcriptional changes associated with reproduction from male-induced effects, which are known to be harmful to females. We found substantial changes in expression of metabolic pathways associated with the activation of reproduction, while male-specific effects were dominated by the onset of an immune response. Changes in female response under different mating strategies was studied using experimental evolution: we found that monogamous females suffered decreased fecundity and their gene expression profiles suggested an overall weaker response to mating. To identify sexually antagonistic genes, we used hemiclonal lines and associated their sex-specific fitness with genome-wide transcript abundance. We confirmed the presence of a negative covariance for fitness and identified a group of candidate genes experiencing sexually antagonistic selection. We then focused on mitochondria, which can enable the accumulation of deleterious mutations with sex-specific effects due to their maternal inheritance, and found few effects on nuclear gene expression in females but major effects in males, predominantly in male-specific tissues. Finally, we used published data to compare intraspecific and interspecific genetic variation for a set of transcripts, to test whether speciation occurs along lines of maximum genetic variance. In conclusion, gene expression techniques can generate useful results in the study of sexual conflict, particularly in association with phenotypic data or when integrated with published datasets.

Thesis (Ph. D.)--North Carolina State University, 2004. / Title from PDF title page (viewed Jan. 22, 2005). Includes vita. Includes bibliographical references.

University, Diss., 2005--Kiel.

Microbes can protect their plant and animal hosts against infection by pathogens, parasites and parasitoids. These ‘defensive microbes' can provide a powerful line of defence beyond the host response and are becoming attractive candidates for disease control. In this thesis, I investigated how defensive microbes can interact with pathogens over evolutionary time by measuring the effects of co-passaging a defensive microbe (Enterococcus faecalis) and a pathogen (Staphylococcus aureus) within the Caenorhabditis elegans model host. In Chapter 1, I found that co-passaging drove the evolution of reduced pathogen virulence as a by-product of adaptation to microbe-mediated defence. Moreover, I show that the mechanism of pathogen resistance to the defensive microbe can determine the direction of virulence evolution. In chapter two, I discovered that the co-passaged defensive microbe and pathogen populations had undergone coevolutionary interactions within host populations via fluctuating selection dynamics. I then showed that these dynamics resulted in patterns of pathogen local adaptation and increased genetic divergence. Finally, in chapter three, I revealed that these coevolutionary interactions significantly affected the costs and benefits of the defensive microbes to their hosts, but that the relationship between these costs and benefits prevented the transition of defensive microbes across the mutualism-parasitism continuum. Together, this thesis uncovers the potential for defensive microbes to shape the evolution of pathogens and demonstrates that defensive microbes can be an evolutionarily dynamic but stable form of host resistance towards infectious disease. As such, the data presented in this thesis have important implications for how we study host-parasite interactions in nature and question our current understanding of virulence evolution, pathogen local adaptation and the origin of defensive microbes.

abstract: The pattern and strength of genetic covariation is shaped by selection so that it is strong among functionally related characters and weak among functionally unrelated characters. Genetic covariation is expressed as phenotypic covariation within species and acts as a constraint on evolution by limiting the ability of linked characters to evolve independently of one another. Such linked characters are "constrained" and are expected to express covariation both within and among species. In this study, the pattern and magnitude of covariation among aspects of dental size and shape are investigated in anthropoid primates. Pleiotropy has been hypothesized to play a significant role in derivation of derived hominin morphologies. This study tests a series of hypotheses; including 1) that negative within- and among-species covariation exists between the anterior (incisors and canines) and postcanine teeth, 2) that covariation is strong and positive between the canines and incisors, 3) that there is a dimorphic pattern of within-species covariation and coevolution for characters of the canine honing complex, 4) that patterns of covariation are stable among anthropoids, and 5) that genetic constraints have been a strong bias on the diversification of anthropoid dental morphology. The study finds that patterns of variance-covariance are conserved among species. Despite these shared patterns of variance-covariance, dental diversification has frequently occurred along dimensions not aligned with the vector of genetic constraint. As regards the canine honing complex, there is no evidence for a difference in the pleiotropic organization or the coevolution of characters of the complex in males and females, which undermines arguments that the complex is selectively important only in males. Finally, there is no evidence for strong or negative pleiotropy between any dental characters, which falsifies hypotheses that predict such relationships between incisors and postcanine teeth or between the canines and the postcanine teeth. / Dissertation/Thesis / Ph.D. Anthropology 2011

The aim of this dissertation is to investigate what role insect-plant interactions play in the formation of host-plant defenses and in the diversification of both groups. We show that various groups of herbivore respond differently to host-plant defenses. Therefore plant defenses diversify into suites of complementary traits, as individual traits fail to provide protection against specialized herbivores. Further, we identify what levels of host-phylogeny shape the food-web structure of insect herbivores. We show that specialized herbivores are affected mainly by the terminal parts of the host-phylogeny. In contrast, more polyphagous guilds are affected mainly by the mid-levels of the host phylogeny because the effects of terminal or deeper phylogeny seem to be surpassed by other factors in more generalist insect species. In the last chapter, we show how specialized insect-plant interactions generated by tight insect-plant coevolution can influence the speciation in plants over environmental gradients.

During the evolution some groups of organisms have become coevolutionary associated with other groups, as is the case of host symbiont systems. To explore coevolutionary history of hosts and their associated symbionts, phylogenetic reconstruction of symbionts and phylogenetic reconstruction of hosts are usually compared. Coevolution is described by coevolutionary events (cospeciation, host switch, duplication, failure to diverge events and linage sorting events). The aim of this work was to test the suitability of MLST method for the complex of entomopathogenic nematodes from the genus Steinernema (with detailed analysis of Steinernema feltiae) and their symbiotic bacteria Xenorhabdus bovienii and subsequently use cophylogenetic comparative analysis to determine their level of cospeciation.

Procedural content generation (PCG) is increasingly used to generate many aspects in a variety of games. AI players, both hand scripted or also generated (by AI methods), are used to evaluate this content. Comparatively little effort is invested in using PCG to generate the whole game, including its rules. In this thesis, we use evolutionary algorithms to generate the game rules, its content and the evaluating AI player on a narrow, but flourishing, genre of endless runners - games where the player is constantly running. For this purpose, we have implemented a framework for creating endless runner games. Our approach could provide more efficiency for game designers, explore completely new game concepts in endless runners, platformer games, and be further generalized to other game genres.

Müllerian mimicry theory postulate that individuals of different species benefit from decreased per-capita attack risks by sharing similar warning signals. In species-rich mimetic assemblages, there is the formation of several distinct sympatric groups of species sharing the same warning signals, often color pattern, called mimetic rings. The coexistence of multiple rings seems paradoxical considering that selection among unpalatable species should favor convergence and thus reinforce a single color pattern. Different rings evolving in distinct habitats could explain the coexistence of multiple mimicry rings. However, the way species use the habitats might influence the emergence of multiple mimicry rings. We combined mathematical modeling and numerical simulations to explore how habitat heterogeneity, abiotic selection and habitat generalist species influence the formation of mimicry rings in a community. We showed that distinct selection pressures, derived from habitat heterogeneity, favored the formation of distinctive mimicry rings. Nevertheless, just the co-existence of species was enough to drive the emergence of the rings. Simulations in which there was just biotic or abiotic selection, time for convergence was faster than when both sources of selection acted together, suggesting conflicting selective pressures exerted by environment and co-existing species. In the presence of species that was habitat generalist, species converged to similar trait values, decreasing the distinctiveness of mimicry rings. A unique mimicry ring was formed if the different habitats optima in the community were very similar or when most species were habitat generalists. Our results suggest that multiple sympatric mimicry rings are formed by a complex interplay between abiotic and biotic selection and is only possible in groups of animals in which local species composition is strongly affected by habitat heterogeneity such as butterflies / No mimetismo Mülleriano, indivíduos de diferentes espécies, ao compartilharem um mesmo sinal de advertência, beneficiam-se mutuamente devido ao menor risco de predação. Em comunidades ricas em mímicos há a formação de grupos simpátricos de espécies denominados anéis miméticos, que compartilham os mesmos sinais de advertência, como por exemplo padrões de coloração. A coexistência de anéis miméticos parece paradoxal, uma vez que, em teoria, a seleção favoreceria a convergência das espécies impalatáveis e, portanto, geraria um único padrão de cor. A evolução de diferentes anéis miméticos em habitats distintos poderia explicar a coexistência desses anéis em uma comunidade. No entanto, a maneira como as espécies utilizam esses habitats talvez influencie também a emergência dos múltiplos anéis miméticos. Utilizamos modelos matemáticos e simulações computacionais para melhor compreender como a heterogeneidade de habitats, a seleção ambiental e espécies generalistas de habitat influenciam a formação de anéis miméticos em uma comunidade. Demonstramos que diferentes pressões seletivas, derivadas de uma heterogeneidade de habitats, podem favorecer a formação de anéis miméticos. Porém, a simples coexistência das espécies é suficiente para a emergência de anéis. Em simulações nas quais só havia seleção imposta por espécies impalatáveis ou pelo ambiente, o tempo de convergência foi mais rápido do que quando as duas forças seletivas atuavam juntas. Isto demonstra que provavelmente há conflito entre a seleção biótica e abiótica, não favorecendo o mesmo ótimo fenotípico. A presença de uma espécie generalista de habitat favoreceu a convergência de espécies para um valor fenotípico similar, diminuindo a distinção entre os anéis. Um único anel foi formado quando os diferentes fenótipos favorecidos pela seleção imposta pelo ambiente eram muito similares entre habitats, ou quando muitas espécies eram generalistas de habitat. Nosso trabalho sugere que múltiplos anéis miméticos simpátricos são formados por uma complexa interação entre seleção biótica e abiótica e que só são possíveis em grupos no qual a diversidade é estruturada em pequenas escalas espaciais, como borboletas